[slicer-users] VMTK centerlines and failure to allocate memory

Ron Kikinis kikinis at bwh.harvard.edu
Mon Jun 14 13:42:05 EDT 2010


Julie,

The centerline algorithm expects as input a triangulated surface model 
and two fiducial lists each containing one fiducial, one for the start 
point, and one for the end point.

You could get to such a surface model by running a segmentation 
algorithm on your data and using the modelmaker to create such a model.

If you want to send me a volume, I can give you more specific advice.

Ron


On 6/14/10 1:02 PM, Julie Rytlewski wrote:
>
> Hello,
>
> I've been unable to successfully run the VMTK centerlines module on my
> image stack--it stops about 40min to an hour into processing with a
> "failure to locate [large number] of bytes." The data consists of 300
> confocal microscopy images (Z-stack), approximately isotropic, 1024x1024
> resolution, 8-bit grayscale. I've tried down-sampling to 512x512--that
> didn't work. I tried taking an ROI from the 512x512 stack with the
> volume cropping module--still didn't work. I've tried down-sampling the
> ROI to somewhere near 256x256--nadda. I've tried deleting all previous
> volumes and loading only the ones necessary for centerlines and that
> didn't help. The vessel enhancement and level sets modules run just
> fine. I'm running this on an iMac with 8GB of RAM.
>
> Are there other options to conserve memory? Or does this module have a
> leak? I'm not convinced that this module is maxing out 8GB of memory...
> or maybe it's not allocating enough to finish processing the data??
>
> Any help or advice would be very much appreciated.
>
> Thanks,
>
> Julie
>
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-- 
Ron Kikinis, M.D.,
Robert Greenes Distinguished Director of Biomedical Informatics
Professor of Radiology, Harvard Medical School
Director, Surgical Planning Laboratory
http://www.spl.harvard.edu/~kikinis



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